K1K2K3 domain of Kgp gingipain

{
  "code": "SASDAF6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis.",
    "publication": {
      "title": "The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis.",
      "author_list": "Li N, Yun P, Jeffries CM, Langley D, Gamsjaeger R, Church WB, Hunter N, Collyer CA",
      "journal": "Mol Microbiol",
      "doi": "10.1111/j.1365-2958.2011.07768.x",
      "pmid": "21812842",
      "published_date": "2011 Sep"
    },
    "status": "released",
    "submitted_date": null,
    "released_date": "2015-07-07"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAF6.out",
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  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAF6_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAF6_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAF6_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAF6.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "KAF 2084 x 2084 SCX CCD",
        "name": "Roper Scientific PI-SCX:4300",
        "resolution": 24.0
      },
      "name": "University of Sydney",
      "city": "Sydney",
      "country": "Australia",
      "beamline_name": "Anton Paar SAXSess",
      "beam_geometry": "Line collimation",
      "type_of_source": "X-ray in house",
      "point_source": false,
      "line_collimation": true,
      "sample_path_length": 1.0,
      "line_collimation_slitlength": 10.0,
      "line_collimation_integrationwidth": 10.0,
      "xray_energy": null,
      "beam_profile_ah": 2.8,
      "beam_profile_al": 1.3
    },
    "sample": {
      "molecule": [
        {
          "long_name": "K1K2K3 adhesin modules of lysine-specific (Kgp) gingipain",
          "short_name": "K1K2K3",
          "sequence": "GPLGSGTTLSESFENGIPASWKTIDADGDGHGWKPGNAPGIAGYNSNGCVYSESFLGGIGVLTPDNYLITPALDLPNGGKLTFWVCAQDANYASEHYAV\r\nYASSTGNDASNFTNALLEETITAKGVRSPKAIRGRIQGTWRQKTVDLPAGTKYVAFRHFQSTDMFYIDLDEVEIKANGKRADFTETFESSTHGEAPAEWT\r\nTIDADGDGQGWLCLSSGQLDWLTAHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINK\r\nGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTMGGSPTPTDYTYTVYRDGTKIKEGLTETTFEEDGVATGNHEYCVE\r\nVKYTAGVSPKKCVNVTVNSTQFNPVQNLTAEQAPNSMDAILKWNAPASKRAEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSS\r\nASYINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTRAQGTWYQKTVQLPAGT\r\nKYVAFRHFGCTDFFWINLDDVVITSGNAPSYTYTIYRNNTQIASGVTETTYRDPDLATGFYTYGVKVVYPNGESAIETATLNITSL",
          "organism": "Porphyromonas gingivalis W83",
          "uniprot_code": "Q51817",
          "uniprot_range_first": 982,
          "uniprot_range_last": 1662,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MRKLLLLIAASLLGVGLYAQSAKIKLDAPTTRTTCTNNSFKQFDASFSFNEVELTKVETK\nGGTFASVSIPGAFPTGEVGSPEVPAVRKLIAVPVGATPVVRVKSFTEQVYSLNQYGSEKL\nMPHQPSMSKSDDPEKVPFVYNAAAYARKGFVGQELTQVEMLGTMRGVRIAALTINPVQYD\nVVANQLKVRNNIEIEVSFQGADEVATQRLYDASFSPYFETAYKQLFNRDVYTDHGDLYNT\nPVRMLVVAGAKFKEALKPWLTWKAQKGFYLDVHYTDEAEVGTTNASIKAFIHKKYNDGLA\nASAAPVFLALVGDTDVISGEKGKKTKKVTDLYYSAVDGDYFPEMYTFRMSASSPEELTNI\nIDKVLMYEKATMPDKSYLEKVLLIAGADYSWNSQVGQPTIKYGMQYYYNQEHGYTDVYNY\nLKAPYTGCYSHLNTGVSFANYTAHGSETAWADPLLTTSQLKALTNKDKYFLAIGNCCITA\nQFDYVQPCFGEVITRVKEKGAYAYIGSSPNSYWGEDYYWSVGANAVFGVQPTFEGTSMGS\nYDATFLEDSYNTVNSIMWAGNLAATHAGNIGNITHIGAHYYWEAYHVLGDGSVMPYRAMP\nKTNTYTLPASLPQNQASYSIQASAGSYVAISKDGVLYGTGVANASGVATVSMTKQITENG\nNYDVVITRSNYLPVIKQIQVGEPSPYQPVSNLTATTQGQKVTLKWEAPSAKKAEGSREVK\nRIGDGLFVTIEPANDVRANEAKVVLAADNVWGDNTGYQFLLDADHNTFGSVIPATGPLFT\nGTASSNLYSANFEYLVPANADPVVTTQNIIVTGQGEVVIPGGVYDYCITNPEPASGKMWI\nAGDGGNQPARYDDFTFEAGKKYTFTMRRAGMGDGTDMEVEDDSPASYTYTVYRDGTKIKE\nGLTATTFEEDGVAAGNHEYCVEVKYTAGVSPKVCKDVTVEGSNEFAPVQNLTGSSVGQKV\nTLKWDAPNGTPNPNPNPNPNPGTTLSESFENGIPASWKTIDADGDGHGWKPGNAPGIAGY\nNSNGCVYSESFGLGGIGVLTPDNYLITPALDLPNGGKLTFWVCAQDANYASEHYAVYASS\nTGNDASNFTNALLEETITAKGVRSPKAIRGRIQGTWRQKTVDLPAGTKYVAFRHFQSTDM\nFYIDLDEVEIKANGKRADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTA\nHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNA\nGDFTVVFEETPNGINKGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDL\nNYILLDDIQFTMGGSPTPTDYTYTVYRDGTKIKEGLTETTFEEDGVATGNHEYCVEVKYT\nAGVSPKKCVDVTVNSTQFNPVQNLTAEQAPNSMDAILKWNAPASKRAEVLNEDFENGIPA\nSWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASHINFEGPQNPDNYLVTPELSLP\nGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTR\nAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITSGNAPSYTYTIYRNNTQIAS\nGVTETTYRDPDLATGFYTYGVKVVYPNGESAIETATLNITSLADVTAQKPYTLTVVGKTI\nTVTCQGEAMIYDMNGRRLAAGRNTVVYTAQGGHYAVMVVVDGKSYVEKLAVK",
          "mw": 73.9,
          "total_mw": 73.9,
          "number_molecules": 1,
          "complex_state": null,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "10 mM TRIS 150 mM NaCl",
        "concentration_unit": "mM",
        "comment": null,
        "additive": "NaCl 150.000 mM",
        "concentration": 10.0,
        "pka": null,
        "ph": 7.6,
        "deuteration": null
      },
      "purity_method": null,
      "name": "K1K2K3 domain of Kgp gingipain",
      "ext_coefficient": null,
      "contrast": 2.982,
      "specific_vol": 0.7374,
      "dry_vol": null,
      "absorbption": 1.823,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
          }
        ],
        "contributor_name": "Cy M",
        "contributor_surname": "Jeffries",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2010-08-15",
    "storage_temperature": 15.0,
    "cell_temperature": 15.0,
    "exposure_time": 10.0,
    "number_of_frames": 1080,
    "wavelength": 0.1542,
    "sample_detector_distance": 0.309,
    "concentration_min": null,
    "concentration_max": 2.83,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.078,
    "s_max": 4.008,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAF6_fit1_model1_img.png",
          "software": "BUNCH",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "mix",
          "software_version": "",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDAF6_fit1_model1.pdb",
          "model_mw": 74.08,
          "bead_radius": 1.9,
          "log": "https://www.sasbdb.org/media/log_files/K1K2K300.log",
          "symmetry": "",
          "comment": "",
          "user": 9
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAF6_fit1_fixed_fit_img.png",
      "software": null,
      "chi_square_value": 1.461742,
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  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": null,
  "i0_calibration_standard": "water",
  "description": "The primary SAXS data displayed in this entry, and subsequent I(0), Rg and p(r) profile, take into account the beam-profile geometry correction (10 mm horizontal slit).",
  "experiment_description": "SAXS data from solutions of K1K2K3 domain of Kgp gingipain in 10 mM TRIS 150 mM NaCl, pH 7.6 were collected using an Anton Paar SAXSess 10 mm line collimated instrument (Sydney University, Australia) equipped with a Roper Scientific PI-SCX:4300 CCD detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.1542 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.83 mg/ml was measured at 15°C. 1080 successive 10 second frames were collected. The data were normalized to the intensity of the transmitted beam and underwent 10 mm horizontal-width integration; the scattering of the solvent-blank was subtracted and the final data were desmeared.",
  "tags": [],
  "intensity_unit": null,
  "experimental_mw": 76.3,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": 0.173,
  "pddf_i0_error": null,
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  "guinier_i0_error": null,
  "pddf_rg": 4.47,
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  "guinier_rg": 4.29,
  "guinier_rg_error": null,
  "pddf_dmax": 14.7,
  "pddf_dmax_error": null,
  "porod_volume": null,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 23,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDAF6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-04-14T11:55:44.084302+02:00",
  "bragg_peak": []
}

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